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Iron in PDB 3ag4: Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.364, 206.648, 178.137, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.9

Other elements in 3ag4:

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K (pdb code 3ag4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3ag4

Go back to Iron Binding Sites List in 3ag4
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:27.0
occ:1.00
 FE A:HEA515 0.0 27.0 1.0
NB A:HEA515 1.9 31.0 1.0
NE2 A:HIS378 1.9 26.3 1.0
NE2 A:HIS61 2.0 26.8 1.0
ND A:HEA515 2.0 26.5 1.0
NC A:HEA515 2.1 27.8 1.0
NA A:HEA515 2.2 27.5 1.0
CE1 A:HIS378 2.9 32.0 1.0
CD2 A:HIS61 2.9 28.6 1.0
C4B A:HEA515 3.0 29.4 1.0
C1B A:HEA515 3.0 28.0 1.0
CD2 A:HIS378 3.0 25.7 1.0
CE1 A:HIS61 3.0 27.9 1.0
C4D A:HEA515 3.0 25.0 1.0
C1D A:HEA515 3.1 24.9 1.0
C1C A:HEA515 3.1 29.7 1.0
C1A A:HEA515 3.1 30.1 1.0
C4C A:HEA515 3.1 29.6 1.0
C4A A:HEA515 3.2 27.8 1.0
CHD A:HEA515 3.4 26.8 1.0
CHC A:HEA515 3.4 23.1 1.0
CHB A:HEA515 3.5 26.7 1.0
CHA A:HEA515 3.5 23.5 1.0
ND1 A:HIS378 4.0 27.3 1.0
CG A:HIS61 4.1 25.7 1.0
ND1 A:HIS61 4.1 25.8 1.0
CG A:HIS378 4.1 26.8 1.0
C3B A:HEA515 4.2 29.4 1.0
C2B A:HEA515 4.2 26.3 1.0
C2D A:HEA515 4.3 23.2 1.0
C3D A:HEA515 4.3 29.5 1.0
C2C A:HEA515 4.3 30.1 1.0
C2A A:HEA515 4.4 27.4 1.0
C3A A:HEA515 4.4 25.1 1.0
C3C A:HEA515 4.4 26.0 1.0
OG A:SER382 4.8 41.1 1.0

Iron binding site 2 out of 4 in 3ag4

Go back to Iron Binding Sites List in 3ag4
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:35.5
occ:1.00
 FE A:HEA516 0.0 35.5 1.0
ND A:HEA516 1.8 27.7 1.0
NB A:HEA516 1.9 35.0 1.0
NC A:HEA516 2.1 34.2 1.0
NA A:HEA516 2.1 30.2 1.0
NE2 A:HIS376 2.1 32.2 1.0
C A:CYN520 2.4 31.3 1.0
N A:CYN520 2.8 31.4 1.0
C4D A:HEA516 2.9 36.5 1.0
C4B A:HEA516 2.9 43.5 1.0
C1C A:HEA516 3.0 30.7 1.0
C1B A:HEA516 3.0 37.6 1.0
C1D A:HEA516 3.0 39.8 1.0
C1A A:HEA516 3.0 29.1 1.0
CE1 A:HIS376 3.0 36.9 1.0
C4A A:HEA516 3.1 29.4 1.0
CD2 A:HIS376 3.1 31.1 1.0
C4C A:HEA516 3.2 34.5 1.0
CHC A:HEA516 3.3 36.8 1.0
CHA A:HEA516 3.3 27.8 1.0
CHB A:HEA516 3.5 34.7 1.0
CHD A:HEA516 3.7 35.0 1.0
C3D A:HEA516 4.1 33.4 1.0
C2B A:HEA516 4.2 33.7 1.0
C3B A:HEA516 4.2 39.4 1.0
ND1 A:HIS376 4.2 31.5 1.0
C2D A:HEA516 4.2 32.7 1.0
CG A:HIS376 4.2 30.4 1.0
C2C A:HEA516 4.3 38.4 1.0
C3A A:HEA516 4.3 24.5 1.0
C2A A:HEA516 4.3 28.9 1.0
C3C A:HEA516 4.3 38.5 1.0
O A:HOH4310 4.7 38.4 1.0
CG2 A:VAL380 4.8 37.4 1.0
CU A:CU517 5.0 31.0 1.0

Iron binding site 3 out of 4 in 3ag4

Go back to Iron Binding Sites List in 3ag4
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:35.5
occ:1.00
 FE N:HEA515 0.0 35.5 1.0
NB N:HEA515 2.0 38.9 1.0
NE2 N:HIS378 2.0 36.8 1.0
NA N:HEA515 2.0 37.0 1.0
NE2 N:HIS61 2.1 30.0 1.0
ND N:HEA515 2.1 32.8 1.0
NC N:HEA515 2.1 35.4 1.0
CE1 N:HIS378 2.9 42.7 1.0
C4B N:HEA515 3.0 38.2 1.0
C1B N:HEA515 3.0 36.6 1.0
C4A N:HEA515 3.0 35.8 1.0
CD2 N:HIS61 3.0 32.9 1.0
C1A N:HEA515 3.0 34.6 1.0
C4D N:HEA515 3.1 32.9 1.0
CE1 N:HIS61 3.1 35.5 1.0
CD2 N:HIS378 3.1 33.3 1.0
C1D N:HEA515 3.1 38.0 1.0
C4C N:HEA515 3.1 39.6 1.0
C1C N:HEA515 3.1 37.3 1.0
CHB N:HEA515 3.4 34.9 1.0
CHA N:HEA515 3.5 31.8 1.0
CHD N:HEA515 3.5 35.0 1.0
CHC N:HEA515 3.6 31.4 1.0
ND1 N:HIS378 4.1 37.8 1.0
C3B N:HEA515 4.2 32.1 1.0
CG N:HIS61 4.2 37.8 1.0
ND1 N:HIS61 4.2 34.0 1.0
CG N:HIS378 4.2 36.0 1.0
C3A N:HEA515 4.2 36.0 1.0
C2A N:HEA515 4.2 30.0 1.0
C2B N:HEA515 4.2 37.4 1.0
C3D N:HEA515 4.3 35.3 1.0
C2D N:HEA515 4.3 35.5 1.0
C3C N:HEA515 4.4 34.5 1.0
C2C N:HEA515 4.4 32.8 1.0
OG N:SER382 4.8 56.9 1.0

Iron binding site 4 out of 4 in 3ag4

Go back to Iron Binding Sites List in 3ag4
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:42.6
occ:1.00
 FE N:HEA516 0.0 42.6 1.0
NB N:HEA516 1.8 36.3 1.0
ND N:HEA516 1.9 37.1 1.0
NA N:HEA516 2.0 40.0 1.0
NC N:HEA516 2.1 42.1 1.0
NE2 N:HIS376 2.2 41.2 1.0
N N:CYN520 2.6 42.3 1.0
C N:CYN520 2.6 43.2 1.0
C4B N:HEA516 2.8 42.8 1.0
C4D N:HEA516 2.9 38.8 1.0
C1A N:HEA516 2.9 34.0 1.0
C1B N:HEA516 3.0 40.1 1.0
CD2 N:HIS376 3.0 38.3 1.0
C1D N:HEA516 3.0 43.4 1.0
C1C N:HEA516 3.1 38.5 1.0
C4A N:HEA516 3.1 38.9 1.0
C4C N:HEA516 3.2 41.4 1.0
CHA N:HEA516 3.3 36.7 1.0
CE1 N:HIS376 3.3 40.8 1.0
CHC N:HEA516 3.4 39.8 1.0
CHB N:HEA516 3.6 39.4 1.0
CHD N:HEA516 3.6 41.3 1.0
C3D N:HEA516 4.1 37.5 1.0
C3B N:HEA516 4.1 35.7 1.0
C2A N:HEA516 4.2 39.1 1.0
C2B N:HEA516 4.2 38.4 1.0
C2D N:HEA516 4.2 35.9 1.0
CG N:HIS376 4.2 39.1 1.0
C3A N:HEA516 4.2 32.9 1.0
ND1 N:HIS376 4.3 38.3 1.0
C2C N:HEA516 4.4 43.0 1.0
C3C N:HEA516 4.4 45.8 1.0
CG2 N:VAL380 4.7 48.3 1.0
O N:HOH4406 4.9 40.0 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Sun Aug 4 07:12:08 2024

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